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Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion(More)
MOTIVATION Although there are several databases storing protein-protein interactions, most such data still exist only in the scientific literature. They are scattered in scientific literature written in natural languages, defying data mining efforts. Much time and labor have to be spent on extracting protein pathways from literature. Our aim is to develop a(More)
Current parallelizing compilers cannot identify a significant fraction of parallelizable loops because they have complex or statically insufficiently defined access patterns. We have previously proposed a framework for their identification. We speculatively executed a loop as a doall, and applied a fully parallel data dependence test to determine if it had(More)
dynamics with NAMD on the IBM Blue Gene/L system S. Kumar C. Huang G. Zheng E. Bohm A. Bhatele J. C. Phillips H. Yu L. V. Kalé NAMD (nanoscale molecular dynamics) is a production molecular dynamics (MD) application for biomolecular simulations that include assemblages of proteins, cell membranes, and water molecules. In a biomolecular simulation, the(More)
MOTIVATION An enormous number of protein-protein interaction relationships are buried in millions of research articles published over the years, and the number is growing. Rediscovering them automatically is a challenging bioinformatics task. Solutions to this problem also reach far beyond bioinformatics. RESULTS We study a new approach that involves(More)
Replication provides a feasible solution for improving data accessibility in highly dynamic and fault prone mobile ad-hoc environments. Efficient replica management, however, remains a challenging problem due to the inherent unreliable and unstable nature of mobile ad-hoc networks. This paper proposes a novel optimistic replication scheme, for achieving(More)
PURPOSE Gliomas are the most frequently occurring primary malignancies in the brain, and glioblastoma is the most aggressive of these tumors. Protein kinase CK2 is composed of two catalytic subunits (α and/or α') and two β regulatory subunits. CK2 suppresses apoptosis, promotes neoangiogenesis, and enhances activation of the JAK/STAT, NF-κB, PI3K/AKT,(More)
Microorganisms such as Pseudomonas putida play important roles in the mineralization of organic wastes and toxic compounds. To comprehensively and accurately elucidate key processes of nicotine degradation in Pseudomonas putida, we measured differential protein abundance levels with MS-based spectral counting in P. putida S16 grown on nicotine or glycerol,(More)
The improved computation presented in this paper is aimed to optimize the neural networks learning process using Levenberg-Marquardt (LM) algorithm. Quasi-Hessian matrix and gradient vector are computed directly, without Jacobian matrix multiplication and storage. The memory limitation problem for LM training is solved. Considering the symmetry of(More)